David Kroll – Terra Sigillatahttp://cenblog.org/terra-sigillata
medicines from the earthSat, 27 Jan 2018 13:14:43 +0000en-UShourly1https://wordpress.org/?v=4.5.1316475936What Are Your Favorite Non-U.S. Drug Discovery Stories?http://cenblog.org/terra-sigillata/2014/06/18/what-are-your-favorite-non-u-s-drug-discovery-stories/
http://cenblog.org/terra-sigillata/2014/06/18/what-are-your-favorite-non-u-s-drug-discovery-stories/#commentsWed, 18 Jun 2014 19:58:48 +0000http://cenblog.org/terra-sigillata/?p=2925 ]]>Over at my other gig at the Pharma & Healthcare section of Forbes.com, I’ve been covering a few stories of new drugs and improvements on old drugs. Although I’m focusing on natural products like vancomycin and semi-synthetics like lurbinectedin, I’ve been thinking a bit about the stories behind the discoveries of all drugs.

Part of my thinking has been driven by my current reading of Happy Accidents: Serendipity in Modern Medical Breakthroughs by Morton A. Meyers, MD, professor emeritus of radiology and internal medicine at SUNY–Stony Brook. Therein, I’m reading stories like that of Gerhard Domagk, who first showed that prontosil was an effective antibiotic in vivo but not in vitro because it liberates sulfanilamide when metabolized. The story was told in even greater detail in the superb Thomas Hager book, The Demon Under the Microscope.

This got me to thinking: I hear quite a bit about drug discovery stories in the U.S. but rarely about modern drugs that have been discovered elsewhere. The brain tumor drug, temozolomide, for example, was developed in the laboratory of Malcolm Stevens at Aston University building upon work of the late Tom Connors (expertly told by Kat Arney at Cancer Research UK last summer). But one rarely hears stories like these, even in pharmacology courses at pharmacy schools where the teaching is more likely to be chemistry-oriented.

So, chemistry world hivemind: What are your favorite stories of drug discovery and development that didn’t occur in the United States? Bonus points for natural products or semi-synthesis.

]]>http://cenblog.org/terra-sigillata/2014/06/18/what-are-your-favorite-non-u-s-drug-discovery-stories/feed/62925Mourning Open Notebook Science Pioneer, Dr. Jean-Claude Bradleyhttp://cenblog.org/terra-sigillata/2014/05/14/mourning-open-notebook-science-pioneer-dr-jean-claude-bradley/
Wed, 14 May 2014 15:16:42 +0000http://cenblog.org/terra-sigillata/?p=2921 ]]>I’ve have more later but I just learned some very sad news from Antony Williams: Drexel University chemist, Jean-Claude Bradley, passed away yesterday.

It is with deep sadness that I inform you of the passing of Jean-Claude Bradley, PhD, associate professor in the Department of Chemistry.

Jean-Claude joined Drexel as an assistant professor in 1996 after receiving his PhD in organic chemistry and serving as a postdoctoral researcher at Duke University and College de France in Paris. In 2004, he was appointed E-Learning Coordinator for Drexel’s College of Arts and Sciences, helping to spearhead the adoption of novel teaching modalities. In that role, he led the University’s initiative to buy an “island” in the virtual world of Second Life, where students and faculty could explore new methods of teaching and learning.

Jean-Claude was most well known for his “Open Notebook Science”(ONS), a term he coined to describe his novel approach to making all primary research (including both successful and failed experiments) open to the public in real time. ONS, he believed—and demonstrated—could significantly impact the future of science by reducing financial and computational restraints and by granting public access to the raw data that shapes scientific conclusions.

“…In the past, trusting people might have been a necessary evil [of research],” Bradley said. “Today, it is a choice. Optimally, trust should have no place in science.”

In June of 2013, Jean-Claude was invited to the White House for an “Open Science Poster Session,” at which he discussed ONS’ role in allowing he and his collaborators to confidently determine the melting points of over 27,000 substances, including many that were never before agreed upon. Currently, his research lab had been working to create anti-malarial compounds to aid in the synthesis of drugs to fight malaria. His lab’s work on this project was made available to the public on a wiki called UsefulChem, which Jean-Claude started in 2005.

Jean-Claude’s philosophy of free, accessible science translated to an open approach in the classroom as well. Content from his undergraduate chemistry courses was made freely available to the public, and real data from the laboratory was used in assignments to practice concepts learned in the classroom.

In an article in Chemistry World last April, Bradley said: “It is only a matter of time before the internet is saturated with free knowledge for all…People will remember those who were first.”

Indeed, we will remember Jean-Claude as a pioneer in the open access movement, an innovative researcher and colleague, and a kind and dedicated educator. His death impacts all who knew him, and especially the students, faculty and collaborators who worked with him daily. For anyone who may need support in dealing with this loss, we encourage you to reach out to the counseling professionals at Drexel’s Counseling Center at 215-895-1415 (or 215-416-3337 after regular business hours).

Our thoughts are with Jean-Claude’s family and friends at this difficult time.

Sincerely,

Donna M. Murasko, PhD
Dean of the College of Arts and Sciences

What a stunning loss of an open chemistry researcher and educator who was also a terrifically kind gentleman.

]]>2921New University of Florida Chemistry Building Is A “Go!” – Againhttp://cenblog.org/terra-sigillata/2014/05/06/new-university-of-florida-chemistry-building-is-a-go-again/
http://cenblog.org/terra-sigillata/2014/05/06/new-university-of-florida-chemistry-building-is-a-go-again/#commentsTue, 06 May 2014 15:28:54 +0000http://cenblog.org/terra-sigillata/?p=2916 ]]>

I’m impressed by the safety goggles and the nitrile gloves. But, um, the reptilian chemist is wearing no pants or protective footwear. It’s the no pants that really troubles me. (Credit: University of Florida, Department of Chemistry)

Well, it’s that time of the academic year to dust off my University of Florida doctoral regalia for this weekend’s commencement activities at my North Carolina institutions. It’s always a delight to be reminded of my graduate school days in UF’s Department of Pharmacology and Therapeutics.

Construction money includes $20 million for a new chemistry building, UF officials said. With the $15 million it received last year and $7 million before that, UF has $42 million toward its needed $60 million to replace the outdated, cramped, chemistry building built in 1947 with one that can meet the growing demand for class and lab space.

The University of Florida has had a chemistry program since the university’s inception in 1906. Master’s degrees were first awarded in 1909 and Ph.D.s in 1930. While the current chemistry facilities are not quite that old, their renovation and replacement are a bit overdue.

In 2008, C&EN ranked Florida among the top 25 U.S. schools producing chemistry graduates at all three levels (C&EN article, 23 November 2009, pg 38, by David J. Hanson).

I’m impressed that the state of Florida has taken advantage of their $1.2 billion budget surplus to reinvest in the state’s higher education system. Both Florida and Florida State are receiving additional funds for recruitment of world-class faculty and will provide faculty raises after five years of no increases. Republican Governor Rick Scott has indicated that he will sign the $77.1 billion budget.

Since I left Gainesville, I’ve continually come across Gator Chemists in my professional travels. Here in North Carolina, I’ve worked with no fewer than three Florida Chemistry Ph.D.s. Much of my contact with chemists during my graduate years was with those in the medicinal chemistry department in the College of Pharmacy, “down the hill” at the J. Hillis Miller Health Center complex, before construction of the new Pharmacy building. But I attended a few seminars at the old chemistry building, usually on my way up to the Purple Porpoise (R.I.P) for oysters, wings, and cheap pitchers of beer.

I’m beside myself with joy to see this pioneering chemist be recognized by the most prominent search engine in the world.

I don’t know where to begin about Julian but I’m sure that many of you have seen The Forgotten Genius, the PBS-produced NOVA life story of the chemist. Julian suffered many indignities in his training, from being denied dormitory residence while earning his B.S. at DePauw University to progression to racial issues limiting him to a M.S. at Harvard. He later completed his Ph.D. work at the University of Vienna in 1931.

Julian is probably best known for using natural products as a template for making drugs. His first major feat, the synthesis of physostigmine, a cholinesterase inhibitor from the Calabar bean used to treat glaucoma has been recognized by ACS as a National Historic Chemical Landmark at DePauw University. This 11-step synthesis from phenacetin, the active metabolite of acetaminophen, was completed with his Vienna colleague, Josef Pikl, and students in the laboratory.

Julian synthesized cortisone, estrogen, progesterone, and testosterone from the Calabar bean compound, stigmasterol. Later, at Glidden Paint Company, a happy accident led Julian to find that soybean extract (soya oil) also contained the 17-member sterol nucleus, a much more accessible source. At this time, we had absolutely no treatments for rheumatoid arthritis. But cortisone, then made by Merck in a laborious 36-step synthesis, was found in 1949 to transform the treatment of rheumatoid arthritis. However, Merck’s starting material was deoxycholic acid from bovine bile. Julian’s synthetic work beginning with sigmasterol.

]]>http://cenblog.org/terra-sigillata/2014/04/11/google-features-percy-julian-legendary-african-american-chemist/feed/22909The Case Of The Malodorous Metabolitehttp://cenblog.org/terra-sigillata/2014/04/06/the-case-of-the-malodorous-metabolite/
http://cenblog.org/terra-sigillata/2014/04/06/the-case-of-the-malodorous-metabolite/#commentsSun, 06 Apr 2014 17:33:27 +0000http://cenblog.org/terra-sigillata/?p=2888 ]]>Over where I also write at Forbes.com, Matthew Herper, Senior Editor for Pharma and Healthcare, reported on GlaxoSmithKline’s NEJM clinical trial of darapladib in coronary artery disease. The drug had been developed as a small molecule, orally-formulated, subnanomolar inhibitor of lipoprotein-associated phospholipase A2.

Lp-PLA2 is associated with apolipoprotein B-containing lipoproteins, such as LDL and non-HDL particles, and is found in the necrotic center of atherosclerotic plaques. Formerly known as platlet-activating factor acetylhydrolase, the enzyme produces pro-apoptotic lysophosphatidylcholine and stimulates the synthesis and release of proinflammatory mediators such as IL-1 beta, IL-6, ICAM-1, and VCAM-1.

A meta-analysis of nearly 80,000 patients across 32 trials indicated that Lp-PLA2 was associated with a relative risk for coronary artery disease of 1.10 for each 1-standard deviation increase in activity, even when correcting for other influences. This magnitude of relative risk is similar to that for non-HDL cholesterol or systolic blood pressure.So, the enzyme seemed like a reasonable target for small-molecule inhibition.

Darapladib (SB-480848) emerged from screening for inhibitors and a synthesis campaign, each published in 2002 and 2003, and was selected for clinical trials. A study with 330 patients with coronary artery disease, The Integrated Biomarkers and Imaging Study-2 trial, showed that 12 months of darapladib (160 mg daily, p.o.) decreased the progression of atherosclerotic plaques that occurred in the placebo group, even when they were also receiving standard-of-care statin therapy.

Last week saw the publication in NEJM of the STABILITY trial to examine efficacy against primary endpoints. Unfortunately, this large, placebo-controlled, randomized trial with 15,828 patients who took 160 mg darapladib once daily showed no benefit of the drug relative to placebo in the primary endpoints of time to cardiovascular death, myocardial infarction, and stroke. However, the drug did show significant differences from placebo in measures of major coronary events (9.3% vs. 10.3 % for placebo) and total coronary events (14.6% vs. 16.1% for placebo).

Major coronary events were defined as “a composite of death from coronary heart disease, myocardial infarction, or urgent coronary revascularization for myocardial ischemia.” Total coronary events were defined as “a composite of death from coronary heart disease, myocardial infarction, hospitalization for unstable angina, or any coronary revascularization procedure.”

But when looking at other aspects of the paper, Herper noted that a small but significant subset of patients reported an unpleasant odor from their skin, urine, or feces while taking darapladib. In discussing the side effects relative to the modest effects on secondary endpoints, Herper wrote,

Would such a small difference be enough to lead cardiologists to prescribe a drug that will leave them fielding tons of calls from patients asking, “Doc, why do I smell so bad?”

What smells?

Of course, I read that paper trying to figure out why the drug or its metabolites might smell unpleasant. No discussion was apparent but I appreciate Herper catching this aspect of the trial.

(Note to my ENG 507 health and environmental writing students at NC State: This is yet another good reason to read the entire paper in pulling out story ideas. Science writer Jennifer Ouelette told last year’s class the she is particularly fond of reading Materials and Methods of papers to find quirky approaches.)

Darapladib and its metabolites. Apologies for the low resolution; this is how it appears in the paper. Credit: Dave et al., Drug Metab Dispos 42:415–430, March 2014.

Only two major CYP-mediated metabolites were detected after oral dosing in human subjects: an N-deethylated metabolite with pharmacological activity (M4, above) and an inactive hydroxylated metabolite (M3). Various gut bacteria incubated under anaerobic conditions failed to produce any significant metabolites.

But the authors also detected an acid hydrolysis product (M10) that liberated 4-fluorobenzyl mercaptan (p-fluorotoluene-α-thiol; CAS 15894-04-9). While they didn’t comment on the smell of this compound, they did note that they ultimately chose to make an enteric-coated darapladib dosage form for clinical trials.

Most readers here would predict this metabolite was the source of the malodor. The relatively low incidence of unpleasant smell from the skin, urine, and feces would be indicative of the general efficacy of the enteric coating and interindividual variations in gastric acidity, emptying time, and patient compliance with the directive to take with food. The metabolite from which 4-fluorobenzyl mercaptan was liberated comprised up to 5% of total metabolites.

Benzyl mercaptan is known to give a smoky odor to wines, but that doesn’t sound particularly unpleasant. It took going to ChemSpider to find any odor characteristics of 4-fluorobenzyl mercaptan. Their citation of Matrix Scientific’s offering of the compound lists hazards as, “TOXIC, STENCH.”

Do any of you have experience with this compound? Would you expect even a small amount of it as a metabolite to be responsible for patient reporting of such an odor?

STABILITY was a robust, large-scale cardiovascular outcomes study of a novel mechanism with the goal of providing incremental benefit above a high level of standard of care. Given the unmet medical need, the results of the STABILITY study are important in understanding how this mechanism may impact the lives of patients with heart disease. We await the results of the second study, SOLID-TIMI 52, to better understand the findings.

The second Phase III study, SOLID-TIMI 52 will evaluate the effects of darapladib in patients with acute coronary syndrome. The trial has enrolled over 13,000 patients across 36 countries. SOLID-TIMI 52 is ongoing and remains blinded. Results are expected in the second quarter of 2014.

We’ll see what comes next and what success investigators have made in minimizing the malodorous metabolite.

]]>http://cenblog.org/terra-sigillata/2014/04/06/the-case-of-the-malodorous-metabolite/feed/22888Colorado Marijuana Product Potency: Just Another Herbal Medicinehttp://cenblog.org/terra-sigillata/2014/03/14/colorado-marijuana-product-potency-just-another-herbal-medicine/
http://cenblog.org/terra-sigillata/2014/03/14/colorado-marijuana-product-potency-just-another-herbal-medicine/#commentsFri, 14 Mar 2014 13:23:09 +0000http://cenblog.org/terra-sigillata/?p=2875 ]]>Since the beginning of the year, I’ve been watching Colorado’s burgeoning legal marijuana economy both as a natural products pharmacologist and science and health journalist and writing professor. And while the Colorado and Washington experiments are interesting to observe from afar, I’m amazed, but not surprised, by how much remains the same when it comes to the chemistry of what is essentially a botanical medicine consumer product.

The Denver Post has made a very concerted effort to treat the legal marijuana market as any economically- and culturally-important area of coverage, going so far as to establishing a focused, online publication called The Cannabist.

Following a less-than-effective personal experience with an edible marijuana product, Baca wondered whether the amount of THC on product labels truly reflect the abundance of the psychoactive component. In Colorado, marijuana “edibles” – technically called marijuana-infused products, or MIPs – are limited to 100 mg of THC, with a recommendation of 10 mg per serving.

Baca solicited the analytical chemistry assistance of one of three state-sanctioned cannabis laboratories, Steep Hill Halent’s Colorado laboratory, directed by chemist Joseph Evans. One particular brand, Dr. J’s, had several products that tested at less than 1 mg of THC despite being labeled at 100 mg.

This JPG shows some of the other results. Some products did quite well – several were spot on at 100 +/- 6 mg – while others were a bit over.

Baca’s reports were picked up widely this week and, as you might expect, received some pushback from companies whose products didn’t fare that well. But he followed up with some explanations from Evans in this article, as well as some additional replicate testing of products procured from a range of retail sites.

But the companies making these products had better get their act together soon. An editorial in The Denver Post on Wednesday reminded manufacturers that Colorado’s potency labeling standards will go into effect on May 1st.

The variation in active principles in each product reminds me of Consumer Reports‘ herbal quality analyses that I’ve used in pharmacy teaching since back in 1996, where they first showed ginsenoside content of U.S. ginseng products varying by two logs.

Steep Hill Halent also provides other product quality testing that you’d want to see in any botanical medicinal product, including tests for pesticide residues and microbial contamination.

Company CEO David Lampach said in a November interview with Marijuana Business Daily that he expects large analytical firms to ultimately outcompete small testing labs as more states inevitably pass recreational marijuana legislation.

Ana Campoy of The Wall Street Journal had anticipated issues with cannabis potency testing in a report last August. Many of us ACS members are familiar with the longstanding work of Mahmoud ElSohly and colleagues at University of Mississippi’s National Natural Products Research Center in producing and analyzing research grade marijuana. Campoy reported that the clash between federal and state regulation of marijuana excluded well-equipped laboratories like ElSohly’s from testing Colorado and Washington products.

So, companies like Steep Hill Halent have wisely stepped in.

Why bother? Lampach estimates that the U.S. cannabis testing market will reach $40 million by 2016.

Hey, Chemjobber! Should we be encouraging our chemistry followers to get some training in cannabinoid analysis?

I had an opportunity earlier this month to write a short “Inside Science” piece for the Charlotte Observer and Raleigh News & Observer newspapers. These two publications are among those under the McClatchy Company umbrella of 30 U.S. newspapers with a history dating back to 1857 and the founding of what is now The Sacramento Bee.

I was offered great latitude in writing a piece that was to run between 401 and 426 words. Our chemblogging community has been debating how best to address public chemophobia – or whether to even use the term “chemophobia” – in emphasizing to general audiences that not all chemicals are toxic at levels to which one is normally exposed.

Just look up and around you. Virtually all life on Earth depends on plants, algae and specialized microbes performing chemical reactions – photosynthesis – that capture the light energy from the sun to produce life-giving chemicals – the unlocking of oxygen from water and the capturing of carbon dioxide from the air to create glucose and other carbohydrates. In most cases, this light-capturing conversion begins with a green pigment in chloroplasts called chlorophyll, itself a magnesium-containing chemical with similarities to heme in our hemoglobin.

I go on to speak, of course, about the massive amount of photosynthesis carried out by phytoplankton and the estimation that about half of the planet’s oxygen results from marine photosynthetic reactions.

And your dear natural products pharmacologist couldn’t resist the urge to speak about secondary metabolites such as indigo and the opiates.

I didn’t count at the time, but the words “chemical” or “chemistry” appeared 16 times in the articles, approximately 4% of the word count.

Writing with a short word limit is very challenging, unlike writing blogposts. Including my self-quote above, this piece runs 463 words without even trying.

Unfortunately for my efforts, these articles received far less attention than I had hoped owing to the West Virginia (4-methylcyclohexane)methanol release a few days later.

But I’d like for these articles to represent how I’m going to approach chemistry education this year. I’ve taken to heart last June’s post by Janet Stemwedel – someone I’ve been learning from since 2005 – that making fun of people who are not well-versed in chemistry or risk assessment is not the best way for us scientists to build trust and promote education.

What do you think? Were my pieces too simple for a regional newspaper audience? And how are you, as a chemistry ambassador, going to reach out to the public in 2014.

]]>http://cenblog.org/terra-sigillata/2014/01/25/promoting-chemistrys-positive-public-image/feed/42838A View on Scientific American Blogs and Censorship of Dr. Danielle Leehttp://cenblog.org/terra-sigillata/2013/10/13/a-view-on-scientific-american-blogs-and-censorship-of-dr-danielle-lee/
http://cenblog.org/terra-sigillata/2013/10/13/a-view-on-scientific-american-blogs-and-censorship-of-dr-danielle-lee/#commentsMon, 14 Oct 2013 02:41:05 +0000http://cenblog.org/terra-sigillata/?p=2812 ]]>For far too long, the presumption has been that if you’re a woman, a person of color, or from a lower socioeconomic status that folks think they can get you, your talent, your expertise, or your energy for free.

Since Friday night, the science blogosphere and larger media enterprises (Buzzfeed, Business Insider) have been abuzz with discussion over the treatment of biologist and science writer Dr. Danielle Lee by the alleged editor of the Biology-Online blog network and, subsequently, censorship by the editor-in-chief of Scientific American.

A recap of the situation is as follows:

1. Danielle receives a query from a person identifying themselves as Ofek, blog editor of Biology-Online.org, which he/she described as “one of the world’s largest biology websites with over 1.6 million visitors per month.”

2. Within 12 hours, Danielle responded that it sounded like a good opportunity but she had questions about the frequency of blogging since it wasn’t exactly clear from Ofek’s original query and another about their payment rate for guest bloggers? (1 and 2 in this correspondence PDF).

3. Ofek responded 10 hours later that he was soliciting a monthly article which Danielle could then repost on her blog after two weeks but that, “Regarding payment, truthfully, we don’t pay guest bloggers.” He/she goes on to say that even Mayo Clinic physician Dr Michael Joyner didn’t receive payment for his one contribution but that one would gain indirect financial benefit from exposure to their 1.6 million monthly visitors.

4. Danielle responded 11 hours later to thank him for his reply, indicated that she would decline his offer, and wished him a good day. (3 and 4 in this correspondence PDF).

At this point, the discussion has been cordial with both parties promptly responding to each others’ queries. But then. . .

5. Ofek responded 11 hours later with a two-line email that read, “Because we don’t pay for blog entries? Are you an urban scientist [the name of her blog] or an urban whore?”

6. Danielle responds eight hours later (Fri 10th October, 8:41 am EDT) with a one-line question, “Did YOU JUST CALL ME A WHORE?” (5 and 6 in this correspondence PDF).

8. Sometime around 10:00 pm on Friday night, the blog post disappears intermittently from Danielle’s blog, and she tweets that she postulates there’s some sort of technical network issue, perhaps due to high traffic. Minutes later, it’s clear that no one can access the blog post.

9. At 10:14 am on Saturday morning, a tweet is posted by Editor in Chief and Senior VP of Scientific American, Mariette DiChristina, that read, “Re blog inquiry: @sciam is a publication for discovering science. The post was not appropriate for this area & was therefore removed.”

10. Much rancor and speculation ensues, in part because Scientific American appears to be selectively penalizing Danielle’s content relative to other bloggers there who post similar kinds of protests or appeals for equity in science and science writing. Biology-Online.org is also listed as a “partner” of Scientific American.

Why, exactly, was the post removed?

So what about Danielle’s post was worthy of censorship by Scientific American?Otherwomen at SciAmBlogs have noted their writing on issues of equity and experiences in the professions. So it can’t be that.

Is it because, out of all her writing and video dialogue, she used one borderline vulgarity (“butt-hurt”)?

It’s found in various conjugations in otherblogposts and even a Fast Company article that SciAm posted. And I’d have to say that its use serves the story and the reader in all the cases where I see it appear.

Now, C&EN prefers that I not use any of George Carlin’s seven words here. But they give me great latitude in writing about topics that affect almost any scientific or personal issue. In fact, I just checked my contract: I’m a non-staff freelancer who has been contracted, “to expand the breadth of coverage and diversity of voices at CENtral Science.”

As for content, the only stipulations are that my work must be my own (other than explicitly-credited guest posts) and that, “the materials produced hereunder do not infringe any copyright violate any property rights or contain any scandalous, libelous or unlawful matter.”

(I double-checked the dictionary to be sure that this post isn’t scandalous, or, “causing general public outrage by a perceived offense against morality or law.”)

CENtral Science blog network is not the 90-year-old magazine that C&EN is – the official organ of the American Chemical Society. CENtral Science is a modern genre extension of the magazine where bloggers who are mostly magazine staff writers can spread their wings and write in a style that doesn’t fit in the magazine yet still serves a subset of their readers.

Some of that content is cleverly fun. Former laser chemist Dr. Lauren Wolf pees in the ocean. She convinced her niece that it’s okay to pee in the ocean. They are now trying to convince her husband that it’s okay to pee in the ocean.

Her post on the concept was a blockbuster here, having some truly superb scientific content and getting picked up by larger and more broad online sites such as Gizmodo and Jezebel. So proud were we of Lauren’s levity that fellow chemist and C&EN reporter Dr. Carmen Drahl did a five-minute interview with Lauren that had a similar, tongue-in-cheek tone. (Postscript: I can personally vouch for the fact that Dr. Wolf doesn’t pee in the wide-open desert of northern New Mexico.)

Hence, I submit that the blog media is different from the more staid, older publications like C&EN, 90 years old this year, and Scientific American, now 168. But it’s the host’s prerogative to define what tone and voice is permitted on the blog network they host (yes, yes, I understand that it’s difficult to fully define contractually.). One would expect, however, that such editorial decisions are applied equally across the network

Where I write at Forbes.com, it’s made very clear that they want me to write on topics within my “swim lane” – pharmaceuticals and drug safety, education, and general science. The one time that I flailed four lanes over – on a weekend – I was politely but firmly told by an editor (within eight hours) that the post was inconsistent with our agreement and that it hadn’t been a problem in the past and they were sure it wouldn’t happen again.

But they did not remove the post.

Why professionals who are men and white still need to stand up for professionals who are women, from other underrepresented groups or, in general, not part of the dominant demographic

In the case of Danielle Lee, it appears that the editorial appropriateness of a post was defined for her differently than for other bloggers at the SciAmBlogs network. Our chemist colleague, Dr. Rubidium, raised the point last night at the irrepressible JAYFK that she feared rules were being inconsistently applied to Danielle because of her being a scientist of color. Dr. Rubidium speaks to this issue from the standpoint of being a chemist who is a woman and a person of color.

I tend to agree with Dr. Rubidium, but for somewhat different reasons. I fear that the selective application of censorship to Danielle’s SciAmBlogs piece was that she wrote in a tone of black, Southern vernacular, with or without an unconscious editorial view of her “blackness.” Danielle herself calls it, “inner city anthropology.” (We can speak elsewhere about acceptable modern terminology to describe people of color as black, Black, brown, or, still in some older parts of my community, yes, Negro.)

I am unapologetically black and urban and female. Why does this matter to science? Because access to science (information and career opportunities) has real life consequences for people. But if the academia doesn’t have representation or at least people who understand these students, then how do they gain access to higher education or STEM?. . .

. . .If I, as a PhD scientist with credentials, cannot call my fellow scientists to task on the role privilege and prejudices play in academia, then who can? Better yet, who else will?

I’m a middle-aged man of only moderate intelligence (1100 math and reading SAT score, 1120 GRE) from a northeastern US white, middle-class family who was fortunate to be given an opportunity for education that I might not have had without the support of a few crucial champions. Whatever that did to me, consciously and unconsciously, is that I’ve spent my independent professional career working on minority scholarships and career development in pharmacy, had a laboratory environment that disproportionately attracted trainees who were women, and spent four years as a pharmaceutical sciences professor at an HBCU in the American South, a region where I’ve now lived for one-third of my life.

So one wouldn’t be surprised to know that I’ve been working on ScienceOnline sessions diversity in the science blogosphere and scientific community for several years. I’ve worked specifically with Danielle Lee since ScienceOnline2011 when she, Alberto Roca (MinorityPostdoc.org) and I co-moderated a session on the underrepresentation of minorities in the STEM discplines and science communications community (in fact, my original proposal for a diversity session held in 2010 included Danielle and the now-silent blogger, AcmeGirl). We subsequently did a similar session in San Jose, California, at the 2011 annual meeting of SACNAS (Society for the Advancement of Chicanos/Hispanics and Native Americans in Science).

And most recently, I worked with Danielle on a Science Journalism 101 panel for the 2013 annual meeting of the National Association of Black Journalists (NABJ) in Orlando, Florida. Together with SciAm editor Robin Lloyd, MedPage Today executive editor Ivan Oransky, and Washington, DC, radio host Jamila Bey, we discussed ways that black-specialty publications might improve their coverage of science and health while encouraging up-and-coming writers of color to pitch science stories.

1. Danielle launches the post about a wrap cloth called a khanga that she wore in Tanzania during her last three-month stint of research there. The English translation of the quote on the khanga is, “Give trouble to others, not me.” This was, in my view, a wonderful metaphor with which to lead the post.

2. She relates this African saying to a 21st century ghetto proverb she learned from growing up in inner South Memphis, “Don’t start none, won’t be none.”

3. She then wrote this paragraph after introducing that Ofek had called her a whore:

My initial reaction was not civil, I can assure you. I’m far from rah-rah, but the inner South Memphis in me was spoiling for a fight after this unprovoked insult. I felt like Hollywood Cole, pulling my A-line T-shirt off over my head, walking wide leg from corner to corner yelling, “Aww hell nawl!” In my gut I felt so passionately:”Ofek, don’t let me catch you on these streets, homie!”

4. After embedding her video response that lacked such vernacular and discussing why anyone would decide not to write compensation-free, she wrote:

But the fact is I told ol’ boy No; and he got all up in his feelings. So, go sit on a soft internet cushion, Ofek, ’cause you are obviously all butt-hurt over my rejection. And take heed of the advice on my khanga.

Thanks to everyone who helped me focus my righteous anger on these less-celebrated equines. I appreciate your support, words of encouragement, and offers to ride down on his *$$.

I’m concerned that the censorship of her post related to editorial discomfort over a woman of color using (mild) inner city language. If that’s one of the reasons, it reflects northern, white discomfort with the way non-northern, non-whites speak.

Two of the most-resonant things Danielle ever said were that when talking to young, black kids about her science, mostly when she was getting her Ph.D. in St. Louis, is that they said she “wasn’t black enough” to be authentic in her call for them to be interested in science – to which she then broke into some good ghetto language that she used to respond to the students.

Second was that she felt we in the sciences tend to underestimate or even disrespect the role that the church plays in the lives of African-Americans. Rather than demonizing religion, as some bloggers and academic do, she felt that reaching out to the religious community would be an effective strategy for scientists to cultivate minority students into our disciplines. Here at CENtral Science, I have to say that I’m proud of some ACS chapters that do just that – a Philadelphia ACS group ran a series of outreach activities at African-American churches to tell the story of the renowned black chemist, Percy Julian.

And while teaching at an HBCU, I fielded scholarship applications where students would unapologetically profess that their pursuit of a pharmaceutical sciences and biotechnology career was a call from God and a way for them to live their faith by doing good works to benefit others.

These kinds of experiences, so common to Danielle and those I have come to understand and appreciate over the last 20 years, lead to a writing style and cultural environment that often makes some white folks uncomfortable.

But for us to be truly inclusive in science – both with regard to recruiting and retaining minority scientists and effectively engaging with underrepresented public audiences – we need to be culturally-sensitive and respectful of the manner in which non-white, non-northern US communities communicate.

Yes, in academic contexts, we are all expected to speak and write in a relatively standardized manner regardless of our backgrounds. But as I mentioned earlier, the blog medium is generally much more informal and inclusive of the thoughts, views, and values that we bring to science communication. The decision to censor Dr. Danielle N. Lee’s blogpost was inconsistent with the medium and, more importantly, the manner in which the writings of other network bloggers are treated.

Note added: It’s been brought to my attention that Stephanie Zvan at Almost Diamonds wrote yesterday on this issue of code-switching and the perception of Danielle’s writing. My apologies for not noticing it until now.

Editorial response update

While I was writing this post, in fits and spurts since 6:15 am, a full explanation was offered by SciAm’s editor in chief, Mariette DiChristina, that Danielle’s post was perceived as a personal issue and, “unfortunately, we could not quickly verify the facts of the blog post and consequently for legal reasons we had to remove the post.” DiChristina then goes on to justify the lack of advance notification of Danielle about the post’s removal with the harried weekend activities. But if one had enough access to remove the post, one would also have the wherewithal to send a three line email to Danielle that they were taking the post down for the weekend, why, and that they would discuss the issue in further detail with her and SciAm bloggers on Monday.

Where’s Bora?

While I read more about the discussion that ensued the rest of Sunday, let me say one thing about the founder and blog editor of SciAm blogs, Bora Zivkovic, in part because he is a local friend and usually a vociferous commentator on a great many issues. I have had no contact with Bora other than to drop him a Twitter DM saying that I would be posting a defense of Danielle and that I would be briefly defending him.

So I can only postulate that he has been working behind the scenes to keep the SciAm blog community informed, unified, and assured that he was working as much as he could on a decision that was probably made up the supervisory chain. Because Bora, like me, left ScienceBlogs.com during the ethical lapse known as Pepsigate, one would expect him to be outraged at the editorial treatment of Danielle’s post. If lawyers became involved, as DiChristina notes, I suspect that Bora had to work very hard to keep his opinions out of the public space.

Bora’s relative silence speaks volumes about how the censorship of Danielle’s post was out of his hands. In fact, I would offer that Scientific American should be very thankful that Bora is their blog network editor because most commentators have given the network the benefit of the doubt because of his integrity. While this episode has blown up, I believe it could be even worse for Scientific American if Bora had not been their blog editor.

Comments and alternative interpretations are always welcome below.

Update: 5:24 am, 14 October – Alan Weisleder of Keebali, the company that operates Biology-Online.org, sent an apology (JPEG screenshot) to Danielle Lee overnight. On their discussion board, a slightly extended apology is directed to the community. Weisleder notes that Ofek was a new employee and has since been terminated.

]]>http://cenblog.org/terra-sigillata/2013/10/13/a-view-on-scientific-american-blogs-and-censorship-of-dr-danielle-lee/feed/62812Nobel Prize in Chemistry 2013 Goes to Karplus, Levitt, and Warshelhttp://cenblog.org/terra-sigillata/2013/10/09/nobel-prize-in-chemistry-2013-goes-to-karplus-levitt-and-warshel/
Wed, 09 Oct 2013 09:49:38 +0000http://cenblog.org/terra-sigillata/?p=2803 ]]>Staffan Normark, Permanent Secretary of the Royal Swedish Academy of Sciences, has just announced Martin Karplus (Strasbourg/Harvard), Michael Levitt (Stanford), and Arieh Warshel (Univ. of Southern California) as this year’s recipients of the chemistry prize, “for the development of multiscale models for complex chemical systems.”

The collective work was described as, “allowing classical and quantum mechanics to shake hands.”

Most relevant to my pharmacology and drug development readers, the laureates developed the computing methods to predict the interaction of pharmaceuticals with their drug targets, allowing drug design in advance of empirical experimentation.

Seven Lidin, Chair of the Nobel Committee for Chemistry said, “There is not a pharmaceutical company that doesn’t have a theory division.”

In 1975 and 1976, Warshel and Levitt began studying how the enzyme lysozyme works. They took the approach of trying to simplify the molecule so as to minimize the amount of computing power required to approximate how the enzyme works.

Warshel was the first to be reached on the Nobel livecast despite being the furthest away (and earliest) at 3:02 a.m. in Los Angeles.

He describes the advance of his work from X-ray crystal structures, static pictures of where atoms sit in three-dimensions. Warshel used the metaphor for X-ray structures of “seeing a watch and wondering how it works.”

Their methodology was a “way which required computers to take a structure of a protein and then to eventually understand how it does what it does.”

Our beloved colleague, Professor Paul Bracher who writes the chemistry blog Chembark, has been liveblogging the proceedings. In a C&EN Nobel predictions roundtable Google Hangout last week, Bracher expressed the feeling that a prize for theoretical work was “a longshot.”

Swedish organic chemist Per-Ola Norrby came the closest out of all the sources I could find in predicting Warshel and Karplus with Norman “Lou” Allinger of the University of Georgia. He notes that Allinger’s work preceded that of all three of this year’s winners.

But to Bracher’s credit otherwise, his odds list did include Monday’s physiology or medicine prize winners – Rothman, Schekman, and Südhof – for a cell biology prize that could have also been awarded in chemistry.

Originally posted on 11 September 2006 at Terra Sigillata on ScienceBlogs.

This post tells you what it means.

Let me tell you about John Michael Griffin, Jr.

Griff, as he was known in high school, was a friend of mine.

Late in the first half of our lives, he stood up for me physically and philosophically, for being a science geek. John’s endorsement was the first time I was ever deemed cool for wanting to be a scientist.

Griff died an engineer and hero in the collapse of one of the World Trade Center towers five [12] years ago today.

We lost touch almost twenty years before, but his kindness and friendship formed not only one of the cornerstones of the scientific life I have today, but in the person and father I have become as well.

—–

At a northern New Jersey Catholic high school in a predominantly Irish town, being a gangly Polish boy from two towns over was not the formula to cultivate one’s popularity or self-preservation.

Throwing the curve in biology and chemistry classes didn’t help either, nor did being a David Bowie fan in a place where Bruce Springsteen was as revered as St. Patrick. That’s probably where the nickname, “Zowie,” came from – the name of the glam rocker’s first child.

Worse, I had skipped a grade in elementary school, and being a year behind physically was not compatible with self-preservation during high school gym class.

But, it was a very simple gesture, sometime in junior year, when one of the packs of scoundrels had me cornered, slamming me against the wall and throwing my books down the hallway. I believe that the offense was that our biology teacher had taken to buying me a Pepsi every time I scored 100 on one of his exams, and I had been enjoying yet another one.

John, already well on his way to his adult height of 6′ 7″ or 6′ 8″, stepped in and said, “Hey, lay off of Zowie. He’s goin’ places.” And with that, the beatings stopped.

I didn’t play sports, at least not any of the ones offered by our school. At that time, soccer hadn’t taken off in the States but I was a huge player and had met John at Giants Stadium in the NJ Meadowlands where I had season tickets (Section 113, row 7, seat 26) for the relocated New York Cosmos. At just $4 a ticket for kids 16 and under, I could afford season tickets to see some of the greatest international soccer stars of the late 20th century: Germany’s Franz Beckenbauer, Italy’s Giorgio Chinaglia, Yugoslavia’s Vladislav Bogiçeviç, and, of course, Brazil’s great Pelé.

All accounts of John as an adult include his devotion to the Giants, NY Rangers, and NY Yankees, but few recall those soccer days. John’s family were long-time Giants season ticket holders and probably got their Cosmos season tickets three rows behind me as some sort of promotional giveaway. I recall that John was surprised that a science dork such as I would be cool enough to know about soccer and come to games myself, my father dropping me off outside the gates so he could go home and watch his beloved football games.

But, we Jersey boys loved soccer at a school where American football and basketball reigned supreme. Many Saturday and Sunday afternoons were spent at the massive stadium during soccer’s American heyday of the late 1970s, with crowds of 50,000 – 75,000 that have yet to be matched today.

—–

Among John’s gifts was the ability to make anything fun and to make anyone laugh. I recall sitting with him in a ski lodge in Amsterdam, NY, as I was recovering from frostbite during an ill-prepared class trip ski weekend. He pulled me into an imaginary board game with a napkin dispenser, where he pretended each napkin contained a message as to how to proceed during each turn. We looked at each other in horror when the waitress came unannounced and cleared our table of the napkins, for some reason John loved to give out wooden watches to his loved ones, he loved sharing and he loved letting the people who he loved how he felt about them.

As a teenager, John was a physical caricature, handsome but a goof, self-effacing but self-confident, and had a clever and caustic wit, both of which he carried into adult professional life and fatherhood. His 15 Sept 2001 missing notice in the Bergen (NJ) Record noted that schoolkids called him, “Barney,” to reflect how they flocked to his presence.

No one was safe from John’s good-hearted and bombastic comedy routines. My father was nicknamed, “Groucho,” by John due to the resemblance of his thick mustache to that of the 1930’s comedian – John would burst spontaneously into seemingly classic Marx Brothers riffs, but with the content imitating my father carrying on about some printing press mishap.

From Class of 1981, St. Mary’s High School, Rutherford, NJ: Clockwise from John with cap in the foreground: Kevin Tormey, Joe McGuire, Matt DiTomasso, Walter Marlowe (valedictorian), Benn O’Hara. Taken at my boyhood home in Wallington on the afternoon between Communion breakfast and evening graduation ceremonies. Griff and DiTomasso ran around Communion breakfast saying, “Party at Kroll’s house.”

My last remembrances of John are half a life away, from the impromptu high school graduation party he called at my house to his pride at finishing his engineering degree and managing facilities for a million-square foot building in Manhattan.

Perhaps he protected me as a kid because he knew that way deep down, he was destined to become an engineering geek himself. And a hero, a much bigger hero, in protecting the lives of others in a very real way.

—–

On the glorious fall morning of 11 Sept 2001, I was fixing coffee for my wife who had been sleeping in when the newsreader on my pager announced that a jet had struck the south tower of the World Trade Center.

I had missed my recent 20-year high school reunion and had not known that John had only months before been appointed director of operations at the WTC by Larry Silverstein’s, Silverstein Properties.

I did not learn until two weeks later that John had facilitated the escape of dozens of workers, handing out wet towels so people could breathe on their way down the stairs. In the 102 Minutes book by New York Times writers Jim Lynch and Kevin Flynn, John is immortalized in the corroborated account of the elevator rescue of 72-year-old Port Authority construction inspector, Tony Savas.

When he returned to 78, Greg Trapp saw a group of three Port Authority employees at work on the doors to the elevator where Tony Savas, a seventy-two-year-old structural inspector, was trapped. Trapp peered into the small gap and saw him, a man with thinning white hair, seemingly serene. One of the workers grabbed a metal easel, wedging the legs into the opening, trying to spread the doors from the bottom, where they seemed to have the greatest leverage. But their efforts had the opposite effect at the top of the doors, which seemed to pinch tighter.

At that moment, John Griffin, who had recently started as the trade center’s director of operations, came over to the elevator bank. At six feet, eight inches tall, Griffin had no problem reaching the top of the door to apply pressure as the others pushed from the bottom. The doors popped apart. Out came Savas, who seemed surprised to find Griffin, his new boss, involved in the rescue. Savas seemed exhilarated, possessed of a sudden burst of energy, rubbing his hands together, or so it seemed to Trapp.

“Okay,” Savas said. “What do you need me to do?”

One of the Port Authority workers shook his head. “We just got you out-you need to leave the building.”

“He was at the back of about 30 people they were evacuating,” his wife, June Griffin, related from the accounts of survivors. “He had been in fires before — he should have gotten out.”

Mrs. Griffin speculated that her husband, instead of running for the exits, headed for the fire control center, where his training as a fire safety officer would have directed him. “He was an engineer,” Mrs. Griffin said. “He must have thought, ‘Buildings don’t just fall down.'”

John also left two daughters, both now teenagers, his parents, a younger brother and older sister, and literally hundreds of friends.

Not just any friends, either – anyone who knew John still says that when he talked with you, it was as though you were the most important person in the world.

—–

Leaving New Jersey in the mid-1980s and running on the tenure-track treadmill 1,600 miles away caused me to stop living life and lose track of a great many friends. I am deeply saddened not to have known John as an adult, a devoted husband and, by all accounts, a remarkable father.

Since John’s death, we’ve all found a little more time in our schedules to make time for one another. As the father of a little girl conceived in the months after the terrorist attacks, I try to respect June’s privacy and just send little gifts for the girls every so often. I cannot imagine how they and nearly 3,000 other families deal privately with the most public of tragedies. There’s this new corporate gifts where you can buy things depending on your budget.

I finally worked up the guts to go to Ground Zero [seven years and] two months ago for the first time. Despite all the bickering about what the memorial should look like, there is a small memorial area set up in the interim. John’s name sits at the top of one column of names on the placards commemorating those lost.

He’ll always be at the top of my list.

John’s wife, June, put up this as her Facebook profile photo this year.

Julie’s memory of the events that took place on 9/11 is spotty. She was a fourth-grader at Crescent Elementary School when relatives came to take her and Jenna home.

“It was kind of chaotic,” Julie recalls, sitting on a stool in her kitchen. “Even though people were saying things, I didn’t know what they were talking about. I didn’t know what terrorism was and not even adults could really grasp what was happening.

“My grandpa came up to me and told me bad people did something to where my dad worked and that’s all I could really grasp at the time.”

After discussing her father’s rescue of Mr. Savas, Julie shared more of her mixed feelings:

“But then I think he actually went back to help more people and I think that’s when the buildings collapsed,” Julie said. “I was kind of angry knowing that he went to go save other people instead of thinking about coming home to his family. That bothered me but now I know he’s a hero.”

As the 10th anniversary of 9/11 approaches, Julie thinks about just some of the many moments she’s missed not having her father around.

“People think that it’s just the anniversaries, birthdays and holidays, and it’s true, those really are hard times, but every day [you have to] keep your head up and think positive,” she said. “It’s little things like learning how to drive and applying for college, or my first day of college that you just kind of wish he was there for, and you just have to keep going, I guess.”

Julie feels that by going after her dreams – which currently means graduating from the University of Tampa and pursuing a career in elementary education – she is making her father proud.

Next Friday, September 20th, many of us are gathering in Rutherford, New Jersey for Griff Rocks On, a fundraiser to honor our fallen hero at our alma mater, St. Mary High School. My sister, Sandi, Class of 1985, designed the announcement for this now sold-out event: